Organisms had to evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here, we have unraveled the bio-chemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, specifically by the ratio between the nucleobases guanine and hypoxanthine. Moreover, we reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogues, which exhibits remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a new mechanism for the morphological and functional diversity of biogenic crystals and may thus inspire the development of genetically designed biomaterials and medical therapeutics.